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The story is about a spaceship sent from Earth that includes a intelligence-enhanced octopus along with regular octopuses. The crew dies, leaving the octopuses to survive and evolve alone. The smart octopus leads the group, mates with one of the non-enhanced octopuses, some of her offspring are intelligent. They survive and return to Earth only to find they are not welcome. They manage to transform an asteroid into their new home and keep going. I think I read the story on one of the annual SF compilation books but can’t remember the name or author. It’s bothering me. Hoping someone recognizes it. Thanks!

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    Are you sure they were octopuses? "Manifold: Time" has a spaceship piloted by an enhanced squid. May 17, 2020 at 20:08

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This looks like another request to find Sheena 5 by Stephen Baxter. According to Wikipedia it was first published in Analog in 2000, and has been republished a number of times, including the 2001 Best Sci-Fi anthology in the link.

As mentioned in the comment above, it's also been incorporated with a few changes into Manifold: Time.

In both iterations Sheena 5 is a (5th generation) intelligent squid who has been picked to land on a near earth asteroid. There is no other crew, Sheena is the sole occupant in both versions of the story.

Unbeknownst to the scientists who sent her off on the mission, Sheena is pregnant, before the mission she lived in a tank with other normal squid, and gives birth to a new generation who go on to inhabit the asteroid. The stories diverge at this point, with the short story having the squid return to earth quite quickly definitely within a human lifetime and the Manifold version having them set off to explore the solar system and then the universe.

Both answers in linked question go into a lot more detail.

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